Contacts of the helix formed by residues 229 - 246 (chain A) in PDB entry 1IZO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ARG* 4.1 0.9 - - - +
222A GLN* 5.3 3.8 + - - -
227A GLN 4.7 1.6 - - - +
228A LEU* 1.3 77.3 - - - +
230A SER* 1.3 66.1 + - - +
231A ARG* 4.2 9.0 - - + +
232A MET* 3.1 13.7 + - + +
233A ALA* 2.9 20.6 + - - +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A GLU* 3.1 22.8 - - - +
198A ILE* 4.2 13.0 - - - +
199A GLU* 3.1 34.1 + - - +
202A ARG* 3.8 18.1 + - - +
228A LEU 3.7 1.0 + - - -
229A ASP* 1.3 72.6 - - - +
231A ARG* 1.3 60.8 + - - +
233A ALA* 3.5 2.4 + - - +
234A ALA* 3.1 22.9 + - - +
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A PRO* 4.7 3.6 + - - +
191A GLU* 3.4 44.5 + - - +
192A GLU* 3.4 34.4 + - - +
195A GLU* 3.1 30.1 + - - +
229A ASP* 3.2 6.1 - - + +
230A SER* 1.3 80.4 - - - +
232A MET* 1.3 56.6 + - - +
234A ALA* 3.2 5.0 + - - +
235A ILE* 2.8 39.8 + - + +
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Residues in contact with MET 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL 4.2 9.9 - - - +
82A ASN* 3.6 15.9 - - - +
83A ALA* 3.3 24.0 - - + -
95A ARG* 3.3 20.0 - - - +
228A LEU* 4.2 12.3 - - + -
229A ASP* 3.1 23.0 + - + +
231A ARG* 1.3 76.8 - - - +
233A ALA* 1.3 60.9 + - - +
235A ILE* 3.1 12.9 + - + +
236A GLU* 2.8 67.4 + - - +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 3.9 24.2 - - + -
202A ARG* 4.0 7.4 - - - +
217A MET* 3.6 27.6 - - - +
228A LEU* 3.9 14.7 - - + +
229A ASP 2.9 16.1 + - - +
230A SER 3.8 4.3 - - - +
232A MET* 1.3 76.1 - - - +
234A ALA* 1.3 57.8 + - - +
236A GLU* 3.4 2.7 + - - +
237A LEU* 2.9 29.1 + - - +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.9 10.1 - - - +
194A ILE* 3.7 14.7 - - + +
195A GLU* 3.6 31.6 - - + +
198A ILE* 4.0 3.1 - - + +
230A SER 3.1 14.6 + - - +
231A ARG* 3.2 11.7 - - - +
233A ALA* 1.3 75.1 - - - +
235A ILE* 1.3 65.3 + - - +
237A LEU* 3.3 2.3 + - - +
238A ILE* 3.0 30.9 + - + +
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Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE 3.8 12.9 - - - +
80A GLY* 4.0 3.6 - - - -
81A VAL* 4.2 23.6 - - + +
83A ALA* 3.7 16.2 - - + -
187A ARG* 4.4 2.0 - - - +
191A GLU* 3.5 39.0 - - + +
231A ARG* 2.8 34.8 + - + +
232A MET* 3.1 27.1 + - + +
234A ALA* 1.3 72.4 - - - +
236A GLU* 1.3 59.2 + - - +
238A ILE* 3.2 11.2 + - - +
239A ASN* 2.9 26.0 + - - +
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Residues in contact with GLU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.6 2.8 - - - +
84A ILE* 3.2 10.2 + - - +
95A ARG* 2.8 28.3 + - + +
98A LEU* 5.1 1.6 - - + -
99A PHE* 3.2 52.6 - - + -
217A MET* 4.0 13.7 - - + -
228A LEU* 4.7 6.1 - - + -
232A MET* 2.8 41.6 + - + +
233A ALA* 3.7 5.6 - - - +
235A ILE* 1.3 76.3 - - - +
237A LEU* 1.3 64.4 + - - +
239A ASN* 2.8 39.2 + - - -
240A VAL* 3.5 3.1 + - - +
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A VAL* 3.9 14.6 - - + -
194A ILE* 3.7 23.1 - - + -
198A ILE* 4.5 3.4 - - + -
213A ALA* 3.9 30.5 - - + +
214A LEU* 3.4 41.5 - - + +
217A MET* 3.8 9.8 - - + +
233A ALA 2.9 16.7 + - - +
234A ALA 3.3 4.5 + - - +
236A GLU* 1.3 74.4 - - - +
238A ILE* 1.3 59.7 + - - +
240A VAL* 2.9 22.9 + - + +
241A LEU* 2.9 32.4 + - + +
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 4.3 20.2 - - + -
169A MET* 4.6 6.3 - - + -
187A ARG* 3.9 26.2 - - - +
190A ALA* 3.8 10.5 - - + +
191A GLU* 3.6 47.1 - - + +
194A ILE* 4.0 17.0 - - + -
234A ALA 3.0 20.2 + - - +
235A ILE* 3.3 9.9 - - - +
237A LEU* 1.3 73.1 - - - +
239A ASN* 1.3 55.3 - - - +
240A VAL 2.9 5.8 + - - -
241A LEU* 4.4 7.0 - - + +
242A ARG* 2.9 36.7 + - + +
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Residues in contact with ASN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE 3.1 23.5 + - - +
83A ALA* 3.7 7.3 - - - +
84A ILE* 4.2 0.2 - - - +
85A GLN* 3.0 22.5 + - - +
99A PHE* 4.0 8.0 - - + -
235A ILE 2.9 12.7 + - - -
236A GLU* 2.8 34.7 + - - +
237A LEU 3.2 0.8 - - - -
238A ILE* 1.3 74.7 - - - +
240A VAL* 1.3 57.4 + - - +
242A ARG* 2.8 36.6 + - - +
243A PRO* 3.1 17.4 - - - +
501A HEM 3.7 21.0 - - + +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A PHE* 3.5 29.2 - - + -
102A LEU* 4.6 4.3 - - + -
103A MET* 4.1 12.1 - - + -
149A TRP* 3.7 34.8 - - + -
213A ALA* 4.4 9.2 - - + -
217A MET* 3.6 16.8 - - + -
236A GLU 3.6 7.0 - - - +
237A LEU* 2.9 14.0 + - + +
239A ASN* 1.3 77.6 - - - +
241A LEU* 1.3 63.3 + - + +
243A PRO* 3.1 14.2 - - - +
244A ILE* 3.1 22.8 + - + +
501A HEM 3.7 7.1 - - + +
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ALA* 3.8 35.3 - - + +
147A CYS* 4.3 12.3 - - - +
150A ALA* 4.0 16.2 - - + -
152A VAL* 4.3 7.0 - - + -
166A PHE* 3.7 27.6 - - + -
193A TRP* 5.0 0.2 - - + -
194A ILE* 4.2 22.2 - - + -
237A LEU* 2.9 29.7 + - + +
238A ILE* 4.2 3.1 - - - +
240A VAL* 1.3 76.9 - - + +
242A ARG* 1.3 67.7 + - - +
244A ILE* 3.0 17.3 + - + +
245A VAL* 3.1 17.4 + - + +
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 3.0 38.7 + - - +
79A PHE* 4.8 0.4 - - - -
85A GLN* 4.3 7.5 - - - +
166A PHE* 3.7 35.0 - - + +
169A MET* 4.0 17.0 - - - -
170A VAL* 3.8 15.5 - - + +
187A ARG* 3.4 9.3 - - - +
238A ILE* 2.9 27.5 + - + +
239A ASN* 2.8 31.1 + - - +
241A LEU* 1.3 72.3 - - - +
243A PRO* 1.3 71.9 - - - +
245A VAL* 3.1 6.6 + - - +
246A ALA* 2.9 24.3 + - - +
501A HEM 6.1 1.2 - - - -
601A PAM 2.8 38.8 + - - +
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Residues in contact with PRO 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A ILE 3.4 5.4 - - - +
239A ASN* 3.1 21.5 - - - +
240A VAL 3.1 17.0 - - - +
242A ARG* 1.3 108.4 - - + +
244A ILE* 1.3 64.0 + - - +
246A ALA* 3.1 12.7 + - + +
247A ILE* 3.4 8.5 + - - +
501A HEM 3.3 49.2 - - + +
601A PAM 3.8 15.5 - - + +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A LEU* 4.4 13.0 - - + -
142A LEU* 3.3 20.2 - - + +
145A VAL* 5.8 1.1 - - + -
146A ALA* 3.8 31.0 - - + +
149A TRP* 3.7 32.3 - - + -
240A VAL* 3.1 22.2 + - + +
241A LEU* 3.0 7.2 + - + +
243A PRO* 1.3 76.4 - - - +
245A VAL* 1.3 59.2 + - - +
247A ILE* 3.0 35.3 + - + +
368A ILE* 4.9 4.9 - - + -
372A VAL* 5.7 2.7 - - + -
501A HEM 3.7 25.4 - - + -
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LYS* 3.9 19.3 - - + +
142A LEU* 3.8 9.4 - - - +
143A CYS* 3.5 35.4 - - + +
146A ALA* 4.9 2.5 - - + -
163A ALA* 4.3 5.4 - - - +
166A PHE* 4.0 24.0 - - + -
167A ILE* 3.8 24.4 - - + +
241A LEU 3.1 11.6 + - - +
242A ARG 3.1 8.1 + - - +
244A ILE* 1.3 76.5 - - - +
246A ALA* 1.3 52.6 + - - +
247A ILE 3.0 1.1 + - - -
248A SER* 2.7 32.6 + - - -
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 4.3 4.5 - - - -
170A VAL* 3.9 13.5 - - + -
242A ARG 2.9 12.5 + - - +
243A PRO* 3.4 11.0 - - + +
244A ILE 3.1 0.6 - - - -
245A VAL* 1.3 73.8 - - - +
247A ILE* 1.3 60.8 + - - +
248A SER* 2.9 10.5 + - - -
249A TYR* 3.1 21.0 + - - -
289A PHE* 3.6 15.8 - - + -
501A HEM 3.7 4.5 - - + -
601A PAM 3.9 26.9 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il